13
Fast, accurate species tree estimation with ASTRID Pranjal Vachaspati
Fast, accurate species tree estimation with ASTRID
Pranjal Vachaspati
ASTRID estimates species trees
INPUT: Gene treesOUTPUT: Species tree computed from internode distance matrices
Similar approach to NJst (Liu & Yu, 2011)
Internode distance matrices
Distance methods for species tree estimationDistance methods take a distance matrix as input, and output a species tree
NJst (predecessor to ASTRID) used neighbor-joining
ASTRID normally uses FastME-2 (Lefort, Desper & Gascuel 2015)
- Faster than neighbor-joining- More accurate
Can also use other methods (BIONJ*, RapidNJ, UPGMA*) in certain cases
Evaluating ASTRID with simulated data
High accuracy on datasets with ILS
47-taxon simulated data based on avian biological dataset
High ILS (47% AD - average distance between true gene trees and true species tree)
High accuracy on datasets with ILS
37-taxon simulated data based on avian biological dataset
Moderate ILS (29% AD - average distance between true gene trees and true species tree)
ASTRID is extremely fastSimulated ILS dataset from ASTRAL-II paper (Mirarab & Warnow, 2015)
1000 gene trees, high ILS
Completes in just 30 seconds!
Competing methods much slower: ASTRAL 5.7.3 took 90 seconds for 100 taxa, 2 hours for 1000 taxa
ASTRID can scale to extremely large datasets43,183 taxon supertree dataset based on RNAsim simulation
ASTRID completed in 5 hours 42 minutes (FastME+NNIs as distance method)
Running time dominated by distance method
- with RapidNJ, only 25 minutes! (but worse accuracy)
High RAM requirements - 132 GB for FastME analysis.
ASTRAL could not run (ran out of memory); MRL took over 24 hours
Getting ASTRID: github.com/pranjalv123/ASTRIDAvailable for Linux, Mac, and Windows
GPL-licensed
Using ASTRIDEasy-to-use command line interface, similar to ASTRAL:
ASTRID -i <input tree file> -o <output tree file>
Usually, this is sufficient!
ASTRID: accurate, extremely fast species tree estimation
Available at github.com/pranjalv123/ASTRID
Join the ASTRID user group at
https://groups.google.com/d/forum/astrid-users or [email protected]
Summary
Using ASTRID: multi-individual datasetsCreate a file mapping individual names to species names:
<file:species_mapping.txt>species1:indiv1,indiv2,indiv3species2:indiv4,indiv5…
ASTRID -i input.trees -o output.trees -a species_mapping.txt
